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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 443 by mmeineke, Wed Apr 2 22:19:03 2003 UTC vs.
Revision 855 by mmeineke, Thu Nov 6 22:01:37 2003 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstring>
1 > #include <stdlib.h>
2 > #include <string.h>
3 > #include <math.h>
4  
5 + #include <iostream>
6 + using namespace std;
7  
8   #include "SimInfo.hpp"
9   #define __C
# Line 9 | Line 12 | SimInfo* currentInfo;
12  
13   #include "fortranWrappers.hpp"
14  
15 + #ifdef IS_MPI
16 + #include "mpiSimulation.hpp"
17 + #endif
18 +
19 + inline double roundMe( double x ){
20 +  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21 + }
22 +          
23 +
24   SimInfo* currentInfo;
25  
26   SimInfo::SimInfo(){
27    excludes = NULL;
28    n_constraints = 0;
29 +  nZconstraints = 0;
30    n_oriented = 0;
31    n_dipoles = 0;
32 +  ndf = 0;
33 +  ndfRaw = 0;
34 +  nZconstraints = 0;
35    the_integrator = NULL;
36    setTemp = 0;
37    thermalTime = 0.0;
38 +  currentTime = 0.0;
39    rCut = 0.0;
40 +  origRcut = -1.0;
41 +  ecr = 0.0;
42 +  origEcr = -1.0;
43 +  est = 0.0;
44 +  oldEcr = 0.0;
45 +  oldRcut = 0.0;
46  
47 +  haveOrigRcut = 0;
48 +  haveOrigEcr = 0;
49 +  boxIsInit = 0;
50 +  
51 +  resetTime = 1e99;
52 +
53 +  orthoTolerance = 1E-6;
54 +  useInitXSstate = true;
55 +
56    usePBC = 0;
57    useLJ = 0;
58    useSticky = 0;
# Line 29 | Line 61 | SimInfo::SimInfo(){
61    useGB = 0;
62    useEAM = 0;
63  
64 +  myConfiguration = new SimState();
65  
33 –
66    wrapMeSimInfo( this );
67 + }
68 +
69 +
70 + SimInfo::~SimInfo(){
71 +
72 +  delete myConfiguration;
73 +
74 +  map<string, GenericData*>::iterator i;
75 +  
76 +  for(i = properties.begin(); i != properties.end(); i++)
77 +    delete (*i).second;
78 +    
79 + }
80 +
81 + void SimInfo::setBox(double newBox[3]) {
82 +  
83 +  int i, j;
84 +  double tempMat[3][3];
85 +
86 +  for(i=0; i<3; i++)
87 +    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
88 +
89 +  tempMat[0][0] = newBox[0];
90 +  tempMat[1][1] = newBox[1];
91 +  tempMat[2][2] = newBox[2];
92 +
93 +  setBoxM( tempMat );
94 +
95 + }
96 +
97 + void SimInfo::setBoxM( double theBox[3][3] ){
98 +  
99 +  int i, j;
100 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
101 +                         // ordering in the array is as follows:
102 +                         // [ 0 3 6 ]
103 +                         // [ 1 4 7 ]
104 +                         // [ 2 5 8 ]
105 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
106 +
107 +  
108 +  if( !boxIsInit ) boxIsInit = 1;
109 +
110 +  for(i=0; i < 3; i++)
111 +    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
112 +  
113 +  calcBoxL();
114 +  calcHmatInv();
115 +
116 +  for(i=0; i < 3; i++) {
117 +    for (j=0; j < 3; j++) {
118 +      FortranHmat[3*j + i] = Hmat[i][j];
119 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
120 +    }
121 +  }
122 +
123 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
124 +
125 + }
126 +
127 +
128 + void SimInfo::getBoxM (double theBox[3][3]) {
129 +
130 +  int i, j;
131 +  for(i=0; i<3; i++)
132 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
133 + }
134 +
135 +
136 + void SimInfo::scaleBox(double scale) {
137 +  double theBox[3][3];
138 +  int i, j;
139 +
140 +  // cerr << "Scaling box by " << scale << "\n";
141 +
142 +  for(i=0; i<3; i++)
143 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
144 +
145 +  setBoxM(theBox);
146 +
147 + }
148 +
149 + void SimInfo::calcHmatInv( void ) {
150 +  
151 +  int oldOrtho;
152 +  int i,j;
153 +  double smallDiag;
154 +  double tol;
155 +  double sanity[3][3];
156 +
157 +  invertMat3( Hmat, HmatInv );
158 +
159 +  // check to see if Hmat is orthorhombic
160 +  
161 +  oldOrtho = orthoRhombic;
162 +
163 +  smallDiag = fabs(Hmat[0][0]);
164 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
165 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
166 +  tol = smallDiag * orthoTolerance;
167 +
168 +  orthoRhombic = 1;
169 +  
170 +  for (i = 0; i < 3; i++ ) {
171 +    for (j = 0 ; j < 3; j++) {
172 +      if (i != j) {
173 +        if (orthoRhombic) {
174 +          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
175 +        }        
176 +      }
177 +    }
178 +  }
179 +
180 +  if( oldOrtho != orthoRhombic ){
181 +    
182 +    if( orthoRhombic ){
183 +      sprintf( painCave.errMsg,
184 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
185 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
186 +               orthoTolerance);
187 +      simError();
188 +    }
189 +    else {
190 +      sprintf( painCave.errMsg,
191 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
192 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
193 +               orthoTolerance);
194 +      simError();
195 +    }
196 +  }
197 + }
198 +
199 + double SimInfo::matDet3(double a[3][3]) {
200 +  int i, j, k;
201 +  double determinant;
202 +
203 +  determinant = 0.0;
204 +
205 +  for(i = 0; i < 3; i++) {
206 +    j = (i+1)%3;
207 +    k = (i+2)%3;
208 +
209 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
210 +  }
211 +
212 +  return determinant;
213 + }
214 +
215 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
216 +  
217 +  int  i, j, k, l, m, n;
218 +  double determinant;
219 +
220 +  determinant = matDet3( a );
221 +
222 +  if (determinant == 0.0) {
223 +    sprintf( painCave.errMsg,
224 +             "Can't invert a matrix with a zero determinant!\n");
225 +    painCave.isFatal = 1;
226 +    simError();
227 +  }
228 +
229 +  for (i=0; i < 3; i++) {
230 +    j = (i+1)%3;
231 +    k = (i+2)%3;
232 +    for(l = 0; l < 3; l++) {
233 +      m = (l+1)%3;
234 +      n = (l+2)%3;
235 +      
236 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
237 +    }
238 +  }
239 + }
240 +
241 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
242 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
243 +
244 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
245 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
246 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
247 +  
248 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
249 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
250 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
251 +  
252 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
253 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
254 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
255 +  
256 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
257 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
258 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
259 + }
260 +
261 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
262 +  double a0, a1, a2;
263 +
264 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
265 +
266 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
267 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
268 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
269 + }
270 +
271 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
272 +  double temp[3][3];
273 +  int i, j;
274 +
275 +  for (i = 0; i < 3; i++) {
276 +    for (j = 0; j < 3; j++) {
277 +      temp[j][i] = in[i][j];
278 +    }
279 +  }
280 +  for (i = 0; i < 3; i++) {
281 +    for (j = 0; j < 3; j++) {
282 +      out[i][j] = temp[i][j];
283 +    }
284 +  }
285 + }
286 +  
287 + void SimInfo::printMat3(double A[3][3] ){
288 +
289 +  std::cerr
290 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
291 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
292 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
293 + }
294 +
295 + void SimInfo::printMat9(double A[9] ){
296 +
297 +  std::cerr
298 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
299 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
300 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
301 + }
302 +
303 +
304 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
305 +
306 +      out[0] = a[1] * b[2] - a[2] * b[1];
307 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
308 +      out[2] = a[0] * b[1] - a[1] * b[0];
309 +      
310 + }
311 +
312 + double SimInfo::dotProduct3(double a[3], double b[3]){
313 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
314 + }
315 +
316 + double SimInfo::length3(double a[3]){
317 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
318 + }
319 +
320 + void SimInfo::calcBoxL( void ){
321 +
322 +  double dx, dy, dz, dsq;
323 +
324 +  // boxVol = Determinant of Hmat
325 +
326 +  boxVol = matDet3( Hmat );
327 +
328 +  // boxLx
329 +  
330 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
331 +  dsq = dx*dx + dy*dy + dz*dz;
332 +  boxL[0] = sqrt( dsq );
333 +  //maxCutoff = 0.5 * boxL[0];
334 +
335 +  // boxLy
336 +  
337 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
338 +  dsq = dx*dx + dy*dy + dz*dz;
339 +  boxL[1] = sqrt( dsq );
340 +  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
341 +
342 +
343 +  // boxLz
344 +  
345 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
346 +  dsq = dx*dx + dy*dy + dz*dz;
347 +  boxL[2] = sqrt( dsq );
348 +  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
349 +
350 +  //calculate the max cutoff
351 +  maxCutoff =  calcMaxCutOff();
352 +  
353 +  checkCutOffs();
354 +
355 + }
356 +
357 +
358 + double SimInfo::calcMaxCutOff(){
359 +
360 +  double ri[3], rj[3], rk[3];
361 +  double rij[3], rjk[3], rki[3];
362 +  double minDist;
363 +
364 +  ri[0] = Hmat[0][0];
365 +  ri[1] = Hmat[1][0];
366 +  ri[2] = Hmat[2][0];
367 +
368 +  rj[0] = Hmat[0][1];
369 +  rj[1] = Hmat[1][1];
370 +  rj[2] = Hmat[2][1];
371 +
372 +  rk[0] = Hmat[0][2];
373 +  rk[1] = Hmat[1][2];
374 +  rk[2] = Hmat[2][2];
375 +  
376 +  crossProduct3(ri,rj, rij);
377 +  distXY = dotProduct3(rk,rij) / length3(rij);
378 +
379 +  crossProduct3(rj,rk, rjk);
380 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
381 +
382 +  crossProduct3(rk,ri, rki);
383 +  distZX = dotProduct3(rj,rki) / length3(rki);
384 +
385 +  minDist = min(min(distXY, distYZ), distZX);
386 +  return minDist/2;
387 +  
388   }
389  
390 + void SimInfo::wrapVector( double thePos[3] ){
391 +
392 +  int i;
393 +  double scaled[3];
394 +
395 +  if( !orthoRhombic ){
396 +    // calc the scaled coordinates.
397 +  
398 +
399 +    matVecMul3(HmatInv, thePos, scaled);
400 +    
401 +    for(i=0; i<3; i++)
402 +      scaled[i] -= roundMe(scaled[i]);
403 +    
404 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
405 +    
406 +    matVecMul3(Hmat, scaled, thePos);
407 +
408 +  }
409 +  else{
410 +    // calc the scaled coordinates.
411 +    
412 +    for(i=0; i<3; i++)
413 +      scaled[i] = thePos[i]*HmatInv[i][i];
414 +    
415 +    // wrap the scaled coordinates
416 +    
417 +    for(i=0; i<3; i++)
418 +      scaled[i] -= roundMe(scaled[i]);
419 +    
420 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
421 +    
422 +    for(i=0; i<3; i++)
423 +      thePos[i] = scaled[i]*Hmat[i][i];
424 +  }
425 +    
426 + }
427 +
428 +
429 + int SimInfo::getNDF(){
430 +  int ndf_local;
431 +  
432 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
433 +
434 + #ifdef IS_MPI
435 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
436 + #else
437 +  ndf = ndf_local;
438 + #endif
439 +
440 +  ndf = ndf - 3 - nZconstraints;
441 +
442 +  return ndf;
443 + }
444 +
445 + int SimInfo::getNDFraw() {
446 +  int ndfRaw_local;
447 +
448 +  // Raw degrees of freedom that we have to set
449 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
450 +  
451 + #ifdef IS_MPI
452 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
453 + #else
454 +  ndfRaw = ndfRaw_local;
455 + #endif
456 +
457 +  return ndfRaw;
458 + }
459 +
460 + int SimInfo::getNDFtranslational() {
461 +  int ndfTrans_local;
462 +
463 +  ndfTrans_local = 3 * n_atoms - n_constraints;
464 +
465 + #ifdef IS_MPI
466 +  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
467 + #else
468 +  ndfTrans = ndfTrans_local;
469 + #endif
470 +
471 +  ndfTrans = ndfTrans - 3 - nZconstraints;
472 +
473 +  return ndfTrans;
474 + }
475 +
476   void SimInfo::refreshSim(){
477  
478    simtype fInfo;
479    int isError;
480 +  int n_global;
481    int* excl;
482  
483 <  fInfo.box[0] = box_x;
44 <  fInfo.box[1] = box_y;
45 <  fInfo.box[2] = box_z;
483 >  fInfo.dielect = 0.0;
484  
485 <  fInfo.rlist = rList;
486 <  fInfo.rcut = rCut;
487 <  fInfo.rrf = ecr;
50 <  fInfo.rt = ecr - est;
51 <  fInfo.dielect = dielectric;
485 >  if( useDipole ){
486 >    if( useReactionField )fInfo.dielect = dielectric;
487 >  }
488  
489    fInfo.SIM_uses_PBC = usePBC;
490    //fInfo.SIM_uses_LJ = 0;
# Line 64 | Line 500 | void SimInfo::refreshSim(){
500  
501    excl = Exclude::getArray();
502  
503 + #ifdef IS_MPI
504 +  n_global = mpiSim->getTotAtoms();
505 + #else
506 +  n_global = n_atoms;
507 + #endif
508 +
509    isError = 0;
510  
511 < //   fInfo;
512 < //   n_atoms;
513 < //   identArray;
72 < //   n_exclude;
73 < //   excludes;
74 < //   nGlobalExcludes;
75 < //   globalExcludes;
76 < //   isError;
511 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
512 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
513 >                  &isError );
514  
78 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
79 –                  &nGlobalExcludes, globalExcludes, &isError );
80 –
515    if( isError ){
516  
517      sprintf( painCave.errMsg,
# Line 91 | Line 525 | void SimInfo::refreshSim(){
525             "succesfully sent the simulation information to fortran.\n");
526    MPIcheckPoint();
527   #endif // is_mpi
528 +
529 +  this->ndf = this->getNDF();
530 +  this->ndfRaw = this->getNDFraw();
531 +  this->ndfTrans = this->getNDFtranslational();
532   }
533  
534 +
535 + void SimInfo::setRcut( double theRcut ){
536 +
537 +  rCut = theRcut;
538 +  checkCutOffs();
539 + }
540 +
541 + void SimInfo::setDefaultRcut( double theRcut ){
542 +
543 +  haveOrigRcut = 1;
544 +  origRcut = theRcut;
545 +  rCut = theRcut;
546 +
547 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
548 +
549 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
550 + }
551 +
552 + void SimInfo::setEcr( double theEcr ){
553 +
554 +  ecr = theEcr;
555 +  checkCutOffs();
556 + }
557 +
558 + void SimInfo::setDefaultEcr( double theEcr ){
559 +
560 +  haveOrigEcr = 1;
561 +  origEcr = theEcr;
562 +  
563 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
564 +
565 +  ecr = theEcr;
566 +
567 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
568 + }
569 +
570 + void SimInfo::setEcr( double theEcr, double theEst ){
571 +
572 +  est = theEst;
573 +  setEcr( theEcr );
574 + }
575 +
576 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
577 +
578 +  est = theEst;
579 +  setDefaultEcr( theEcr );
580 + }
581 +
582 +
583 + void SimInfo::checkCutOffs( void ){
584 +
585 +  int cutChanged = 0;
586 +  
587 +  if( boxIsInit ){
588 +    
589 +    //we need to check cutOffs against the box
590 +
591 +    //detect the change of rCut
592 +    if(( maxCutoff > rCut )&&(usePBC)){
593 +      if( rCut < origRcut ){
594 +        rCut = origRcut;
595 +        
596 +        if (rCut > maxCutoff)
597 +          rCut = maxCutoff;
598 +  
599 +          sprintf( painCave.errMsg,
600 +                    "New Box size is setting the long range cutoff radius "
601 +                    "to %lf at time %lf\n",
602 +                    rCut, currentTime );
603 +          painCave.isFatal = 0;
604 +          simError();
605 +      }
606 +    }
607 +    else if ((rCut > maxCutoff)&&(usePBC)) {
608 +      sprintf( painCave.errMsg,
609 +               "New Box size is setting the long range cutoff radius "
610 +               "to %lf at time %lf\n",
611 +               maxCutoff, currentTime );
612 +      painCave.isFatal = 0;
613 +      simError();
614 +      rCut = maxCutoff;
615 +    }
616 +
617 +
618 +    //detect the change of ecr
619 +    if( maxCutoff > ecr ){
620 +      if( ecr < origEcr ){
621 +        ecr = origEcr;
622 +        if (ecr > maxCutoff) ecr = maxCutoff;
623 +  
624 +          sprintf( painCave.errMsg,
625 +                    "New Box size is setting the electrostaticCutoffRadius "
626 +                    "to %lf at time %lf\n",
627 +                    ecr, currentTime );
628 +            painCave.isFatal = 0;
629 +            simError();
630 +      }
631 +    }
632 +    else if( ecr > maxCutoff){
633 +      sprintf( painCave.errMsg,
634 +               "New Box size is setting the electrostaticCutoffRadius "
635 +               "to %lf at time %lf\n",
636 +               maxCutoff, currentTime  );
637 +      painCave.isFatal = 0;
638 +      simError();      
639 +      ecr = maxCutoff;
640 +    }
641 +
642 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
643 +    
644 +    // rlist is the 1.0 plus max( rcut, ecr )
645 +    
646 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
647 +    
648 +    if( cutChanged ){
649 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
650 +    }
651 +    
652 +    oldEcr = ecr;
653 +    oldRcut = rCut;
654 +    
655 +  } else {
656 +    // initialize this stuff before using it, OK?
657 +    sprintf( painCave.errMsg,
658 +             "Trying to check cutoffs without a box. Be smarter.\n" );
659 +    painCave.isFatal = 1;
660 +    simError();      
661 +  }
662 +  
663 + }
664 +
665 + void SimInfo::addProperty(GenericData* prop){
666 +
667 +  map<string, GenericData*>::iterator result;
668 +  result = properties.find(prop->getID());
669 +  
670 +  //we can't simply use  properties[prop->getID()] = prop,
671 +  //it will cause memory leak if we already contain a propery which has the same name of prop
672 +  
673 +  if(result != properties.end()){
674 +    
675 +    delete (*result).second;
676 +    (*result).second = prop;
677 +      
678 +  }
679 +  else{
680 +
681 +    properties[prop->getID()] = prop;
682 +
683 +  }
684 +    
685 + }
686 +
687 + GenericData* SimInfo::getProperty(const string& propName){
688 +
689 +  map<string, GenericData*>::iterator result;
690 +  
691 +  //string lowerCaseName = ();
692 +  
693 +  result = properties.find(propName);
694 +  
695 +  if(result != properties.end())
696 +    return (*result).second;  
697 +  else  
698 +    return NULL;  
699 + }
700 +
701 + vector<GenericData*> SimInfo::getProperties(){
702 +
703 +  vector<GenericData*> result;
704 +  map<string, GenericData*>::iterator i;
705 +  
706 +  for(i = properties.begin(); i != properties.end(); i++)
707 +    result.push_back((*i).second);
708 +    
709 +  return result;
710 + }
711 +
712 + double SimInfo::matTrace3(double m[3][3]){
713 +  double trace;
714 +  trace = m[0][0] + m[1][1] + m[2][2];
715 +
716 +  return trace;
717 + }

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